Reproductive success among ancient Icelanders stratified by ancestry

iceland-pca

New paper (behind paywall), Ancient genomes from Iceland reveal the making of a human population, by Ebenesersdóttir et al. Science (2018) 360(6392):1028-1032.

Abstract and relevant excerpts (emphasis mine):

Opportunities to directly study the founding of a human population and its subsequent evolutionary history are rare. Using genome sequence data from 27 ancient Icelanders, we demonstrate that they are a combination of Norse, Gaelic, and admixed individuals. We further show that these ancient Icelanders are markedly more similar to their source populations in Scandinavia and the British-Irish Isles than to contemporary Icelanders, who have been shaped by 1100 years of extensive genetic drift. Finally, we report evidence of unequal contributions from the ancient founders to the contemporary Icelandic gene pool. These results provide detailed insights into the making of a human population that has proven extraordinarily useful for the discovery of genotype-phenotype associations.

icelanders
Shared drift of ancient and contemporary Icelanders. (A) Scatterplot of D-statistics reflecting Iceland-specific drift. To aid interpretation, we included values for ancient British-Irish Islanders and a subset of contemporary individuals (who were correspondingly removed from the reference populations).

We estimated the mean Norse ancestry of the settlement population (24 pre-Christians and one early Christian) as 0.566 [95% confidence interval (CI) 0.431–0.702], with a nonsignificant difference betweenmales (0.579) and females (0.521). Applying the same ADMIXTURE analysis to each of the 916 contemporary Icelanders, we obtained a mean Norse ancestry of 0.704 (95% CI 0.699–0.709). Although not statistically significant (t test p = 0.058), this difference is suggestive. A similar difference ofNorse ancestry was observed with a frequency-based weighted least-squares admixture estimator (16), 0.625 [Mean squared error (MSE) = 0.083] versus 0.74 (MSE = 0.0037). Finally, the D-statistic test D(YRI, X; Gaelic, Norse) also revealed a greater affinity between Norse and contemporary Icelanders (0.0004, 95% CI 0.00008–0.00072) than between Norse and ancient Icelanders (−0.0002, 95% CI −0.00056–0.00015). This observation raises the possibility that reproductive success among the earliest Icelanders was stratified by ancestry, as genetic drift alone is unlikely to systematically alter ancestry at thousands of independent loci (fig. S10). We note that many settlers of Gaelic ancestry came to Iceland as slaves, whose survival and freedom to reproduce is likely to have been constrained (17). Some shift in ancestry must also be due to later immigration from Denmark, which maintained colonial control over Iceland from 1380 to 1944 (for example, in 1930 there were 745 Danes out of a total population of 108,629 in Iceland) (18).

icelander-admixture
Shared drift of ancient and contemporary Icelanders. (B) Estimated Norse,
Gaelic, and Icelandic ancestry for ancient Icelanders using ADMIXTURE
in supervised mode.

Five pre-Christian Icelanders (VDP-A5, DAVA9, NNM-A1, SVK-A1 and TGS-A1) fall just outside the space occupied by contemporary Norse in Fig. 3A. That these individuals show a stronger signal of drift shared with contemporary Icelanders is also apparent in the results of ADMIXTURE, run in supervised mode with three contemporary reference populations (Norse, Gaelic, and Icelandic) (Fig. 3B). The correlation between the proportion of Icelandic ancestry from this analysis and PC1 in Fig. 2A is |r| = 0.913.(…)

(…) as the five ancient Icelanders fall well within the cluster of contemporary Scandinavians (Fig. 3C), we conclude that they, or close relatives, likely contributed more to the contemporary Icelandic gene pool than the other pre-Christians. We note that this observation is consistent with the inference that settlers of Norse ancestry had greater reproductive success than those of Gaelic ancestry.

icelanders-y-dna
Haplogroup data, from the paper. Image modified by me, with those close to Gaelic and British/Irish samples (see above Scatterplot of D-statistics and ADMIXTURE data) marked in fluorescent: yellow closer to Gaelic, green less close.

Ancient Icelanders show a clear relation with the typically Norse Y-DNA distribution: I1 / R1a-Z284 / R1b-U106.

  • Among R1a, the picture is uniformly of R1a-Z284 (at least five of the seven reported).
  • There are six samples of I1, with great variation in subclades.
  • Among R1b-L51 subclades (ten samples), there are U106 (at least one sample), L21 (three samples), and another P312 (L238); see above the relationship with those clustering closely with Gaelic samples, marked in fluorescent, which is compatible with Gaelic settlers (predominantly of R1b-L21 lineages) coming to Iceland as slaves.

Probably not much of a surprise, coming from Norse speakers, but they are another relevant reference for comparison with samples of East Germanic tribes, when they appear.

Also, the first reported Klinefelter (XXY) in ancient DNA (sample ID is YGS-B2).

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Population structure in Argentina shows most European sources of South European origin

argentina-population

Open access Population structure in Argentina, by Muzzio et al., PLOS One (2018).

Abstract (emphasis mine):

We analyzed 391 samples from 12 Argentinian populations from the Center-West, East and North-West regions with the Illumina Human Exome Beadchip v1.0 (HumanExome-12v1-A). We did Principal Components analysis to infer patterns of populational divergence and migrations. We identified proportions and patterns of European, African and Native American ancestry and found a correlation between distance to Buenos Aires and proportion of Native American ancestry, where the highest proportion corresponds to the Northernmost populations, which is also the furthest from the Argentinian capital. Most of the European sources are from a South European origin, matching historical records, and we see two different Native American components, one that spreads all over Argentina and another specifically Andean. The highest percentages of African ancestry were in the Center West of Argentina, where the old trade routes took the slaves from Buenos Aires to Chile and Peru. Subcontinentaly, sources of this African component are represented by both West Africa and groups influenced by the Bantu expansion, the second slightly higher than the first, unlike North America and the Caribbean, where the main source is West Africa. This is reasonable, considering that a large proportion of the ships arriving at the Southern Hemisphere came from Mozambique, Loango and Angola.

argentina-pca
Principal component analysis.
On the x axis is PC 1 while PC2 is the y axis. Plus symbols represent Argentinian samples and circles are for reference panels. Fig 2a (left) Argentinians with YRI and LWK for African references (“African”), IBS and TSI for European references (“European”) and the PEL, MXL, PUR and CLM as a Latin American references. Fig 2b (right) samples from Argentina with IBS, MXL, CLM and PEL.

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Pre-Roman and Roman mitogenomes from Southern Italy

vagnari-cemetery-haplogroups-superimposed

Ph.D. thesis Assessing Migration and Demographic Change in pre-Roman and Roman Period Southern Italy Using Whole-Mitochondrial DNA and Stable Isotope Analysis, or The Biogeographic Origins of Iron Age Peucetians and Working-Class Romans From Southern Italy, by Matthew Emery, McMaster University (2018).

Abstract (emphasis mine):

Assessing population diversity in southern Italy has traditionally relied on archaeological and historic evidence. Although informative, these lines of evidence do not establish specific instances of within lifetime mobility, nor track population diversity over time. In order to investigate the population structure of ancient South Italy I sequenced the mitochondrial DNA (mtDNA) from 15 Iron Age (7th – 4th c. BCE) and 30 Roman period (1st – 4th c. BCE) individuals buried at Iron Age Botromagno and Roman period Vagnari, in southern Italy, and analyzed δ18O and 87Sr/86Sr values from a subset of the Vagnari skeletal assemblage.

Phylogenetic analysis of 15 Iron Age mtDNAs together with 231 mtDNAs spanning European prehistory suggest that southern Italian Iapygians share close genetic affinities to Neolithic populations from eastern Europe and the Near East. Population pairwise analysis of Iron Age, Roman, and mtDNA datasets spanning the pan-Mediterranean region (n=357), indicate that Roman maternal genetic diversity is more similar to Neolithic and Bronze Age populations from central Europe and the eastern Mediterranean, respectively, than to Iron Age Italians. Genetic distance between population age categories imply moderate mtDNA turnover and constant population size during the Roman conquest of South Italy in the 3rd century BCE.

In order to determine the local versus non-local demographic at Vagnari, I measured the 87Sr/86Sr and 18O/16O of composition of 43 molars, and the 87Sr/86Sr composition of an additional 13 molars, and constructed a preliminary 87Sr/86Sr variation map of the Italian peninsula using disparate 87Sr/86Sr datasets. The relationship between 87Sr/86Sr and previously published δ18O data suggest a relatively low proportion of migrants lived at Vagnari (7%).

This research is the first to generate whole-mitochondrial DNA sequences from Iron Age and Roman period necropoleis, and demonstrates the ability to gain valuable information from the integration of aDNA, stable isotope, archaeological and historic evidence.

italy-iron-age-mtdna
mtDNA haplogroup composition between Botromagno (7th – 4th century BCE; n=15) and Vagnari (1st – 4th century CE; n=30) skeletal assemblages.

Interesting excerpts:

Taken together, population pairwise ΦST, and the distribution of mtDNA haplotypes in relation to the comparative mtDNA data set show that the Iron Age southern Italians likely descended from early to late Neolithic farmers from Anatolia and possibly as far East as the Caucasus, and from migrants arriving from eastern Europe around the late Neolithic/early Bronze Age. These findings support previous hypotheses that the ancestors of the Iapygians may have originated in the eastern Balkan region, or derive shared ancestry with a common source population from eastern Europe. Alternatively, southern Italian Iron Age mtDNA variation might also reflect LGM gene flow between southwestern European, Mediterranean, and Carpathian basin refugia, which was suggested for haplogroup subclusters of U5 and J (Malyarchuk et al., 2010; Pala et al., 2012). Future mtDNA (and nuclear DNA) analysis comprised of a larger Iron Age data set from southern Italy is necessary to answer Theodor Mommsen’s initial hypothesis that the Iapygians were the oldest immigrants to the southern Italian region.

Our investigation provides the first mtDNA evidence for the maternal ancestral affiliations of a subset of the Iapygian individuals recovered from southern Italy, and suggests a closer genetic link to European Neolithic and Iron Age Armenians, than to Bronze Age Aegeans. Future comparative ancient DNA data using whole-genome SNP, mtDNA, and NRY-chromosome analysis of pre-Roman populations will provide complementary evidence for the ancestral roots of understudied Iron Age individuals from Italy.

Illyrian_colonies_in_Italy_550_BC
Simplistic map of Illyrian colonies in Italy 550 BCE, from Wikipedia

Archaeological evidence indicates that the Iapygians traded and incorporated Hellenistic elements into their material and cultural traditions (Small, 1992; Peruzzi, 2016). These changes are most apparent in burial custom and ceramic production, and become increasingly prominent by 2400 BP (Peruzzi, 2016). Further evidence shows that Iron Age communities across South Italy retracted in size amidst ongoing conflict between colonies in Magna Graecia, and Rome and Carthage (Small, 1992). This apparent change was interpreted as a decline in local populations throughout the region. However, Bayesian Skygrid analysis using the mtDNA profiles of 15 Iapygians and 30 Roman period individuals suggest that female effective population size was comparable between the two populations. In Chapter 4, population distance (measured as population pairwise ΦST values) across a range of mtDNAs obtained from the pan-Mediterranean, European, and western Asian regions suggest closer maternal affinities to Neolithic and Bronze Age populations from the eastern Mediterranean as a cohort, than with Iron Age Italians. This finding points to moderate mtDNA turnover, and is likely the consequence of Roman gene flow stemming from central and northern Italy via the migration and subsequent occupation by Roman colonies after 2250 BP.

Roman Imperial pursuits peaked by ~2050 BP. This extension of power, coupled with an increase in food and materials procurement, was driven by a substantial labour force comprised of both low status Romans and slaves (Harris, 1980; Bradley, 1987, 1994, 2000). Although several attempts have been made to quantify the number of slaves required to maintain the Roman economy, it is unknown what fraction of the Roman population was slave-owned (~approximately 1 to 3 million by 2050 BP) (Scheidel, 2005). Rome’s slave acquisition during the early centuries of the Republic was likely maintained through military campaigns and conquest, a trend that is well documented in Italy (Scheidel, 1997, 1999, 2005; Harris, 1999; Small, 2002). However, once territory was secured, local slave populations were likely maintained through one or a combination of the following: i) the importation of slaves from non-local regions, ii) were born to slave-owned parents, or iii) were voluntarily self-enslaved to acquire subsistence (Harris, 1999). The importation of foreign slaves was likely more costly than maintaining a self-reproducing slave population, especially in rural areas. As such, rural Roman necropoleis, such Vagnari, provide an opportune case to determine the local versus non-local demographic. Archaeological evidence suggests that Vagnari was involved in agriculture and industrial procurement, and was likely staffed by low-class individuals possibly including slaves (Small et al., 2000). However, without direct archaeological or epigraphic evidence, it is impossible to identify the proportion of slaves at rural sites.

italy-iron-age-roman-plot
Multi-dimensional scaling plots showing pairwise ΦST values by a) age and b) country. We removed age and geographic categories with less than 5 mtDNA sequence representation to reduce scaling stress, which decreased the sample size from 402 mtDNAs to n = 378 by age, and n= 382 by country. a) MDS plot of the mtDNA categorized by country of origin; b) MDS of mtDNA dataset by age spanning the Upper Paleolithic (pre-LGM) to the Roman period. IronAge 1 = Italian Iron Age samples; IronAge 2 = Armenian Iron Age samples; Roman 1 = Italian Roman samples; Roman 2 = Egyptian Roman samples; TIP = Third Intermediary Period (Egypt); LP = Late Period (Egypt); PP = Ptolemaic Period (Egypt).

(…) The isotope values presented in Chapter 3 obtained from 56 Roman individuals buried at Vagnari suggest that over half (58%) were born directly at Vagnari, with a further 34% originating from South Italy. Only 7% (3/43 with both δ18O and 87Sr/86Sr values) of the individuals sampled resulted in isotope values non-local to the southern peninsula. Two of these individuals originated from either northern Italy or, more broadly, from central Europe, while one individual likely originated from North Africa. Overall, the isotope data suggest a low number of immigrants at Vagnari, which conforms with the population pairwise (ΦST) data for the Iron Age and Roman mtDNAs, and suggests that as the Romans occupied the region, they populated their Imperial properties with people from central Italy (possible the region of Latium, and the surrounding environs of Rome). These results also integrate with the historical evidence concerning the Roman slave economy during the Imperial period. Future research using a larger comparative dataset comprised of pre-Roman and Roman period mtDNAs, δ18O and, 87Sr/86Sr results will refine the interpretations outlined here.

A paper from this thesis is already published in a peer-review journal, Mapping the origins of Imperial Roman workers (1st–4th century CE) at Vagnari, Southern Italy, using 87Sr/86Sr and δ18O variability, Am J Phys Anthropol (2018).

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